Enzymatic template polymerization

ABSTRACT

A conductive polymer is formed enzymatically in the presence of a polynucleotide template. The method includes combining at least one redox monomer with a polynucleotide template and a redox enzyme, such as horseradish peroxidase, to form a reaction mixture. The monomer aligns along the template before or during the polymerization. Therefore, the polynucleotide template thereby affects the molecular weight and conformation of the conductive polymer. When the conductive polymer is complexed to a polynucleotide duplex, the conformation of the polynucleotide duplex can be modulated by changing the oxidation state of the conductive polymer.

RELATED APPLICATION

This is a continuation of U.S. application Ser. No. 09/447,987, filedNov. 23, 1999, which is a continuation-it-part of U.S. application Ser.No. 08/999,542, filed Nov. 21, 1997 (now U.S. Pat. No. 6,018,018), whichis a continuation-in-part of U.S. application Ser. No. 08/915,827, filedAug. 21, 1997 (now U.S. Pat. No. 5,994,498), the entire teachings ofwhich are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with support from the Government under AROCooperative Grant DAAH04-94-2-003. The Government has certain rights inthis invention.

BACKGROUND OF THE INVENTION

Recently, there has been an increased interest in tailored developmentof certain classes of polymers, such as electrically conductive andoptically active polymers (e.g. polythiophene, polypyrrole, polyphenolsand polyaniline) for application to wider ranges of use. Examples ofsuch uses include light-weight energy storage devices, electrolyticcapacitors, anti-static and anti-corrosive coatings for smart windows,and biological sensors. However, the potential applications to whichpolymers can be put have been limited by their lack of solubility andprocessability.

In particular, interest in developing biosensors has been stimulated byefforts to sequence the human genome. Analysis and manipulation ofpolynucleotides is expected to have genetic engineering applications andaid in the diagnosis of genetic disease and in the development andimprovement of new drugs. For example, deoxyribonucleotides (DNA) existin living organisms almost exclusively in a double helix conformation.However, many variations in this conformation has been shown to exist(e.g., A-, B-, C- and Z-type duplexes). The helical structure of aparticular duplex is related to its sequence and its environment. Thesevariations in conformation are thought to be responsible for the bindingof molecular species, such as enzymes or regulatory proteins, to DNA.Therefore, methods of modulating the conformation of DNA are expected tohave applications in the area of biosensors, molecular recognition anddrug development.

SUMMARY OF THE INVENTION

The present invention relates to a composition of matter in which asubstituted or unsubstituted polyaniline is bound to a polynucleotide asa complex. The invention also relates to a method of preparing apolynucleotide/polyaniline complex, wherein thepolynucleotide/polyaniline complex is formed by combining a substitutedor unsubstituted aniline monomer, a polynucleotide template and a redoxenzyme, whereby the aniline monomer aligns along the polynucleotidetemplate to form a complex and polymerizes to form a polyaniline,thereby forming the polynucleotide/polyaniline complex.

Another aspect of the invention is a method of modulating theconformation of a polynucleotide double helix which is bound to aconductive polymer as a complex by changing the oxidation state of theconductive polymer. In a specific embodiment, polyaniline is bound to apolynucleotide double helix as a complex. Oxidation of polyaniline(e.g., increasing the positive charge on the polyaniline) which iscomplexed to a polynucleotide double helix causes the double helix tobecome more tightly wound (i.e., the double helix will have more basepairs per turn after oxidation of the polyaniline). Conversely, reducingthe polyaniline will cause a double helix associated with it to becomemore loosely wound. Therefore, complexation of polyaniline to apolynucleotide double helix provides a method of modulating theconformation of the double helix by changing the oxidation state of thepolyaniline.

The invention also relates to an electrical element that has a nanowireextending from it. The nanowire includes a polynucleotide template and aconductive polymer bound together as a complex.

Another aspect of the invention is a method of forming an electricallyconductive connection between electrical elements. The method includesconnecting at least two electrical elements with a polynucleotide andcontacting the polynucleotide with an a redox monomer and a redoxenzyme. The monomer aligns along the template to form a complex andpolymerizes to form a conductive polymer that is complexed to thepolynucleotide that connects the electrical elements. Thepolynucleotide/conductive polymer complex is electrically conductiveand, therefore, forms an electrically conductive connection between theelectrical elements.

Another embodiment of the invention is a method of identifying a targetpolynucleotide by contacting the target polynucleotide with a probe thatincludes a polynucleotide template complexed with a conductive polymer.The probe hybridizes with the target polynucleotide which causes atleast one electromagnetic property of the conductive polymer to bemodified. The target polynucleotide is identified by detecting themodified electromagnetic property.

In this invention, the polynucleotide can serve at least three criticalfunctions. First, the polynucleotide can serve as a template upon whichthe monomers preferentially align themselves to form a complex, such asa charge-transfer complex, thereby limiting parasitic branching andcontrolling the shape of the polymer. In the case of polyaniline, themechanism of polymerization is primarily para-directed and results information of the electrically active form of polyaniline. Thispreferential alignment provides improved electrical and opticalproperties of the final polymer complex. Second, the polynucleotide canserve as a large molecular dopant species which is complexed andessentially locked to the polyaniline chains. Current limitations to theactual use of polyaniline in electronic and optical applications largelyhas been due to poor dopant stability. Small ionic dopants orchromophores that are currently used are known to diffuse away with timeand/or conditions. Locking of a large polyelectrolyte dopant (e.g., apolynucleotide) to the polymer is significant in that it ensures thatthe electronic nature of the conjugated backbone structure of thepolymer is maintained, and hence the desired electronic and opticalproperties are stabilized. Third, the polynucleotide template canimprove water solubility of the final polynucleotide/polyaniline complexfor environmentally friendly, facile, and inexpensive processing.

In addition to the above advantages, complexation of a polynucleotideduplex, such as DNA, to an electrically conductive polymer provides amethod by which the conformation of the duplex can be modulated, therebyproviding possible application in the area of biosensors and drugdevelopment. For example, changing the oxidation state of polyanilinebound to a DNA duplex changes the linear length of a helical turn and,therefore, could be used to study the binding properties of DNAregulatory proteins.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the general mechanism of enzymatic polymerization ofaniline in the absence of the polynucleotide, promoting ortho- andpara-directed reactions.

FIG. 2 shows the chemical structure of oxidized (conducting) and reduced(insulating) forms of the polyaniline which is formed during enzymatictemplate guided polymerization.

FIG. 3 shows the visible absorption spectra of the polyaniline templatecomplex (0.05M aniline to 0.1M sulfonated polystyrene (SPS)) formed atvarious pH's.

FIG. 4 shows a plot of absorbance versus (SPS)/aniline ratio to find theoptimum dopant-to-monomer ratio.

FIG. 5A shows the visible absorption and redox behavior ofpolyaniline/SPS prepared at pH 4.0 with increasing pH.

FIG. 5B shows the visible absorbance and redox behavior ofpolyanilines/SPS prepared at pH 4.0 with decreasing pH.

FIG. 6A shows the visible absorbance and redox behavior of a 50 bilayerfilm of poly(diallyl dimethyl ammonium chloride) (PDAC) alternating withSPS/polyaniline (prepared at pH 4.0) with increasing pH.

FIG. 6B shows the visible absorbance and redox behavior of a 50 bilayerfilm of SPS/polyaniline (prepared at pH 4.0) with decreasing pH.

FIG. 7A shows the visible absorbance of polyphenol without SPS versusphenol monomer. Polyphenol precipitated out of solution as a result ofpolymerization.

FIG. 7B shows the visible absorbance of polyphenol/SPS template versusphenol monomer. The polyphenol did not precipitate out of solution.

FIG. 8 is a schematic representation of polyaniline bound to a DNAdouble helix.

FIG. 9 shows the UV-Vis spectra of DNA and DNA/polyaniline (Pani) duringpolymerization.

FIG. 10 shows the CD spectra of DNA and DNA/polyaniline duringpolymerization.

FIG. 11 shows the CD spectra of DNA; a mixture of DNA, aniline monomerand horseradish peroxidase (HRP); DNA and NH₄F; and DNA/polyaniline.

FIG. 12A shows the CD spectra of DNA/polyaniline as the pH is increasedfrom 4 to 10.

FIG. 12B shows the CD spectra of DNA/polyaniline as the pH is decreasedfrom 10 to 4.

FIG. 13A shows the UV-Vis spectra of DNA/polyaniline as the pH isincreased from 4 to 10.

FIG. 13B shows the UV-Vis spectra of DNA/polyaniline as the pH isdecreased from 10 to 4.

DETAILED DESCRIPTION OF THE INVENTION

The features and other details of the apparatus and method of theinvention will now be more particularly described and pointed out in theclaims. It will be understood that the particular embodiments of theinvention are shown by way of illustration and not as limitations of theinvention. The principal features of this invention can be employed invarious embodiments without departing from the scope of the invention.All parts and percentages are by weight unless otherwise specified.

Enzyme-catalyzed polymerization of aniline typically involves reactionat the ortho and para positions of the aromatic ring as shown in FIG. 1.This mechanism often results in branched polymeric materials which areintractable and have negligible electrical and optical properties. Thisinvention describes a novel template assisted enzymatic polymerizationwhich results in a new class of polyanilines. In general, thepolyanilines formed by the enzymatic template guided polymerizationdescribed herein are linked at the para-position (see FIG. 2) and,therefore, are less branched than they generally would be as a result ofsome other polymerization method.

In one embodiment, the invention is a composition of matter thatincludes a polynucleotide template and a polyaniline bound together as acomplex. A method of the invention includes preparing apolynucleotide/polyaniline complex by combining an aniline monomer, apolynucleotide template and a redox enzyme. The monomer aligns along thetemplate to form a complex and polymerizes to form polyaniline, therebyforming the polynucleotide/polyaniline complex.

Typically, enzymatic template guided polymerization reactions of theinvention are carried out in water. However, other solvents can beinclude, for example, dimethyl formamide, dimethyl sulfoxide, methanol,ethanol, dioxane, etc. The pH of the solvent is adjusted to a pH in arange of between about 4.0 and about 10.0. Preferably, the pH is betweenabout 4.0 and about 5.0 for aniline monomer. Examples of suitablebuffers include Tris-HCl buffer, sodium phosphate, sodium citrate, etc.When the template used is a polynucleotide, the preferable buffer issodium citrate.

A suitable redox enzyme is added to the reaction mixture. Theconcentration of enzyme in the reaction mixture is sufficient tosignificantly increase the polymerization rate of the monomer in thereaction solution. Typically, the concentration of enzyme in thereaction mixture is in a range of between about one unit/ml and aboutfive units/ml where one unit will form 1.0 mg purpurogallin frompyrogallol in 20 seconds at pH 6.0 at 20° C. Examples of suitableenzymes include peroxidases, laccase, etc. Preferred enzymes areperoxidases. A particularly preferred enzyme is horseradish peroxidase.

Monomers which are suitable for the template polymerization reaction aremonomers which can be polymerized by enzymatic, redox polymerization toform a conductive and/or optical active polymer. Such monomers aredefined herein as “redox monomers”. Examples of suitable redox monomersinclude substituted or unsubstituted anilines and substituted orunsubstituted phenols. Therefore, the polyaniline or polyphenol formedcan be substituted or unsubstituted. The monomer can be a neutralcompound, a cation or an anion. Further, the monomer can be, forexample, a dye, such as an azo compound, or a ligand. Alternatively, anoligomer can be employed rather than a monomer. Mixtures of differentmonomers, oligomers, or of monomers and oligomers, can also be employed.In one embodiment, oligomers can form from the monomer prior toassociation or complexation with a template. The concentration ofmonomer in the reaction mixture generally is in a range of between about0.05 mM and about 100 mM.

A polynucleotide template preferably is present in an amount that atleast causes a portion of the aniline monomer present to bind to thepolynucleotide template and that causes at least a portion of themonomer to polymerize while bound to the template. A “polynucleotidetemplate,” as that term is employed herein, is defined as a nucleotidepolymer or oligomer that can bind, such as by ionic binding, a redoxmonomer before and during polymerization of the monomer, whereby themonomer polymerizes. When aniline is the redox monomer, the templatefacilitates coupling of the aniline monomers predominately at the paraposition of the aromatic ring. It is believed that binding of anilinemonomers can affect polymerization of adjacent monomers along thepolynucleotide template, thereby controlling polymerization, and thatthe negatively charged polynucleotide backbone forms electrostatic bondswith aniline monomers, thus causing them to align along the backbone ofthe polynucleotide template. When the redox monomers are polymerized apolynucleotide/conductive polymer complex is formed. When anilinemonomers are polymerized in the presence of a polynucleotide template apolynucleotide/polyaniline complex is formed.

In alternative embodiments, other polymers or oligomers can be employedas templates for polymerization. For example, sulfonated polystyrene,sulfonated polystyrene polyion salts, polypeptides, proteins, biologicalreceptors, zeolites, caged compounds, azopolymers, and vinyl polymers,such as polyvinyl benzoic acid, polystyrene sulfonic acid and polyvinylphosphonates, poly(vinyl phosphonic acid), etc can be suitabletemplates. The template can be an anion or cation, such as a polyanionor a polycation. Further, the template can be an optically activepolyelectrolyte, for example, azo polymers. The template can also be adendrimer or a compound that forms micelles, for example, dodecylbenzene sulfonic acid. The monomer or oligomer associates with thetemplate to form, for example, a complex. After polymerization, thecomplex can be electrically or optically active.

The polymerization reaction is a redox reaction and typically isinitiated by adding a suitable oxidant, such as a hydrogen peroxidesolution, etc. In one embodiment, the hydrogen peroxide has aconcentration in the polymerization solution in a range of between aboutone millimolar and about five millimolar. To avoid or minimizedenaturation of the enzyme, a dilute solution of hydrogen peroxide canbe prepared from a 30% stock solution and added slowly to the reactionwith stirring. Preferably, the dilute solution of hydrogen peroxide isabout 0.1 M to about 0.001 M. Typically, the reaction mixture ismaintained at a temperature in a range of between about 10° C. and about25° C. during polymerization. More preferably, the temperature of thereaction mixture is maintained at a temperature of about 20° C. duringpolymerization.

The resulting polymer can be, for example, a linear polymer, such as anextended linear polymer intertwined with the template. Alternatively,the polymer can be dendritic, or branched. In any case, the polymer canhave a conformation that would not be produced in the absence of thetemplate.

In one embodiment, the polymer can be polyaniline complexed with apolynucleotide template, wherein the polyaniline is an extended linear,helical or branched polymer intertwined with the polynucleotidetemplate. In a specific embodiment, the polyaniline is a component of awater soluble electrically conducting complex.

Optionally, the method of the invention includes forming a layer of thepolymer on a surface. In this embodiment, the pH of the polymer solutionis reduced to a suitable pH, such as a pH in a range of between about2.0 and about 8.0, by adding a suitable acid, such as hydrochloric acid,etc. A suitable surface, such as a glass slide treated with an alkali,such as Chemsolv® alkali, is immersed in a polymer solution for asufficient period of time to cause the polymer to accumulate at thesurface. In one embodiment, a glass slide is immersed in a polymersolution for about ten minutes and then removed. The surface can then bewashed with water at a pH of about 2.5 in order to remove unboundpolymer from the surface.

Distinct layers of polymers can be applied to a surface by this method.For example, an initial layer can be formed by exposing a suitablesurface to a polymer formed by the method of the invention that is apolyanion and then subsequently exposing the same surface, having thepolyanion deposited upon it, into a solution of a polycation. In onespecific embodiment, a glass slide treated with Chemsolv® alkali isexposed to a one milligram/milliliter solution of poly(diallyl dimethylammonium chloride) at a pH of 2.5 as a polycation, and then exposed to aone milligram/milliliter solution of SPS/polyaniline formed by themethod of the invention, as a polyanion. A bilayer of polymers isthereby formed. Additional layers of these or other polymers cansubsequently be applied.

Polymerization of the template can be initiated simultaneously with, orsubsequent to alignment and polymerization of the bound monomer oroligomer. In one embodiment, the template can be removed from theresulting polymer, such as by decomposition, dissolution, or enzymaticdegradation to leave behind a polymer shell.

In one specific embodiment of the method of the invention, thetemplate-assisted enzymatic polymerization of aniline can be carried outin an aqueous solution using 0.1M sodium phosphate or tris-HCl bufferand a pH ranging from about 4.0 to about 10.0. Aniline monomer typicallycan be added in a range of between about 10 mM and about 100 nM, and anappropriate amount of a template, in this case sulphonated polystyrene(SPS) (molecular weight of 70,000), can be added in ratios ranging fromabout 1:10 to about 10:1 SPS/aniline. The enzyme horseradish peroxidasethen can be added to the reaction mixture in a range of about oneunit/ml to about five units/ml. To initiate the reaction, an oxidizer,such as a 30% solution of hydrogen peroxide, can be added slowly in 10μl increments over a reaction time of 3 hours, with constant stirring toa final concentration ranging from about 10 mM to about 100 mM.

In another specific embodiment of the invention, the template guidedpolymerization of aniline can be carried out using a polynucleotidetemplate. The polynucleotide is dissolved in an aqueous buffer, such asa 10 mM sodium citrate buffer, having a pH of about 4 to about 10.Preferably, the buffer pH is about 4 to about 5. The concentration ofthe polynucleotide can be determined by UV absorption using the molarextinction coefficient of the polynucleotide at a particular wavelength.This gives the concentration of nucleotide bases which make up thepolynucleotide. The molar extinction concentration of a polynucleotidein the polymerization reaction is typically about 1 mM to about 5 mM.Aniline monomer is added to the polynucleotide solution in aconcentration such that the ratio of aniline to nucleotide bases in thepolynucleotide is about 1:10 to about 10:1, more preferably about 1:1.Horseradish peroxidase (HRP) is added to the solution to a concentrationof about 1 unit/mL to about 5 units/mL, then an oxidizer, such ashydrogen peroxide, is added slowly to the reaction mixture to initiatethe reaction. The amount of hydrogen peroxide added is about one-fifthequivalent to about 1.0 equivalents of the aniline monomer in thereaction mixture. The reaction time is typically about 80 min.

In yet another specific embodiment of the method of the invention, thetemplate-assisted enzymatic polymerization of phenol can be carried outin an aqueous solution using 0.1M sodium phosphate or tris-HCl bufferand pH ranging from 4.0 to 10.0. Phenol monomer typically can be addedin a range of between about 10 mM and about 100 mM and an appropriateamount of the template, sulphonated polystyrene (molecular weight of70,000), can be added in ratios ranging from about 1:10 to about 10:1SPS/phenol. The enzyme horseradish peroxidase then can be added to thereaction mixture in a range of about one unit/ml to about five units/ml.To initiate the reaction, an oxidizer, such as a 30% solution ofhydrogen peroxide, can be added slowly in about 10 μl increments over areaction time of about 3 hours with constant stirring to a finalconcentration ranging from about 10 mM to about 100 mM.

It is to be understood that polymers formed by the method of theinvention can be formed in an oxidized, electrically conducting form orin a reduced, insulating form of the polymer (see FIG. 2). Otherphysical properties of the polymers that can be affected by the methodof the invention include the molecular weight and shape of the polymer.It is also to be understood that the polymers formed by the method ofthe invention can be modified after polymerization. For example,modification call be made at amine functional groups to form amides orimine groups.

Dissolved polymers formed by the method of the invention can beprecipitated from solution by adjusting the pH with a suitable acid orbase. Examples of suitable acids or bases include hydrochloric acid,sodium hydroxide, etc.

In a preferred embodiment, a polynucleotide duplex can be used as atemplate for polymerization of polyaniline. Polynucleotide duplexes havea handedness and, therefore, may impose a chirality on the polyanilineto which they are complexed. Alternatively, the polyaniline complexed toa polynucleotide duplex may be achiral.

The conformation of the polynucleotide duplex complexed to a conductivepolymer can be controlled by controlling the degree of oxidation of theconductive polymer. In general, the more positive charges the backboneof the conductive polymer carries, the more tightly wound the doublehelix will be. For example, the conformation of the polynucleotideduplex in a polynucleotide/polyaniline complex can be controlled bycontrolling the degree of oxidation of the polyaniline. When polyanilineis in the conducting, or oxidized, form, where the polyaniline isprotonated (see FIG. 2), the polynucleotide duplex is more tightly wound(e.g., has more base pairs per helical repeat) than when polyaniline isin the insulating, or reduced form, where the polyaniline is neutral.Polyaniline can be converted from the insulating form to the conductingform by adding protons to (or subtracting electrons from) thepolyaniline backbone. This oxidation process is called “doping” thepolyaniline. Conversely, the polyaniline can be dedoped, or reduced, bysubtracting protons from (or adding electrons to) the polyanilinebackbone. When a polynucleotide/polyaniline complex is in solution, itcan be doped (oxidized) by decreasing the pH of the solution, or dedoped(reduced) by increasing the pH of the solution.

Alternatively, the polyaniline in the complex can be doped or dedopedelectrochemically using, for example, a potentiostat/galvanostat set-up.The potentiostat/galvanostat set-up can have, for example, athree-electrode cell with platinum wire as the working electrode,Ag/AgCl as the reference electrode and platinum mesh as thecounter-electrode. The polynucleotide/polyaniline complex can becontained in an electrolyte solution, such as a sodium citrate bufferhaving about 0.1 M ammonium chloride in contact with the workingelectrode. The doping and dedoping process may be observed by cyclingthe potential between about −0.02 V and 0.8 V with respect to theAg/AgCl electrode.

Therefore, the conformation of the polynucleotide duplex in apolynucleotide/polyaniline complex can be modulated by changing theoxidation state of the polyaniline. After oxidation or reduction of thepolyaniline, the polynucleotide duplex can recover its originalconformation, or substantially the same conformation as its originalconformation, by returning the polyaniline to its original, or near itsoriginal oxidation state. A polynucleotide duplex has substantially thesame conformation if the conformation, as determined by circulardichroism (hereinafter “CD”), is at least about 75% the same.

Another embodiment of the invention is an electrical component. Theelectrical component includes an electrical element, such as, a voltagesource, a resistor, a capacitor, an inductor, a diode, a switch or atransistor, which is attached to one or more nanowires. A nanowire, asthat term is employed herein, includes a polynucleotide and a conductivepolymer, such as polyaniline, bound together as a complex.

The polynucleotide in the nanowire can be a single strand, a doublehelix or a portion of the polynucleotide can be a single strand and aportion of the polynucleotide can be a double helix. In addition, thepolynucleotide can be a deoxyribonucleotide, a ribonucleotide, apolynucleotide analog, a modified polynucleotide or an oligonucleotide.Also encompassed within the invention are polynucleotides that are acombination of deoxyribonucleotide, a ribonucleotide, a polynucleotideanalog, a modified polynucleotide and an oligonucleotide.

An electrical element can be connected to one or more other electricalelements by a nanowire. The electrical elements can be connected to eachother in a closed electrical path, or a path that can be closed by anelectrical switching element, to form a circuit. When the nanowire isused to connect two or more electrical elements, the nanowire can beself-assembled by hybridization. In this embodiment, each electricalelement has one or more polynucleotides attached to it, a portion ofwhich can hybridize to a portion of a polynucleotide on a differentelectrical element. Alternatively, a polynucleotide connector which canhybridize a portion of the sequence of two or more polynucleotides thatare attached to different electrical elements can be use to connect thetwo elements. The polynucleotide connector can be one or morepolynucleotides. When the connector is composed of more than onepolynucleotide, at least a portion of each polynucleotide that makes upthe connector is hybridized to one or more other polynucleotides in theconnector.

The polynucleotide is attached to a surface of the electrical element byderivatizing the polynucleotide with a group that can bind to thesurface. Therefore, selection of a functional group with which thepolynucleotide is to be derivatized is dependent on the type of materialto which the polynucleotide is to be attached. When the polynucleotideis to be attached to a surface on an electrical element which is gold,silver, copper, cadmium, zinc, palladium, platinum, mercury, lead, iron,chromium, manganese, tungsten, or any alloys of the above metals, thepolynucleotide to be attached is preferably derivatized with a thiol,sulfide or disulfide group. When the surface to which the polynucleotideis to be attached is doped or undoped silica, alumina, quartz or glass,the polynucleotide is preferably derivatized with a carboxylic acid.When the surface to which the polynucleotide is to be attached isplatinum or palladium, the polynucleotide is preferably derivatized witha nitrile or isonitrile group. Finally, when the surface to which thepolynucleotide is to be attached is copper, the polynucleotide ispreferably derivatized with a hydroxamic acid group.

The invention also relates to a method of forming an electricallyconductive connection between one or more electrical elements. Theelectrically conductive connection is formed by connecting two or moreelectrical elements with a polynucleotide. The polynucleotide iscontacted with a redox monomer, such as an aniline monomer, and a redoxenzyme, whereby the redox monomer aligns along the polynucleotide and ispolymerized. The polynucleotide/conductive polymer complex (nanowire)formed connects the electrical elements and is electrically conductive.

The polynucleotide connecting two or more electrical elements canself-assemble by hybridization. In this embodiment, the entirepolynucleotide, or a portion thereof, that is attached to an electricalelement, hybridizes to a complementary, or substantially complementary,polynucleotide, or a portion of a polynucleotide, attached to adifferent electrical element. The specificity of hybridization allowsspecific connections between electrical elements to be predetermined bydetermining the sequence of the polynucleotide attached to eachelectrical element. The polynucleotides hybridize forming thepredetermined connections when they are combined in a solution havingthe appropriate conditions of temperature and chemical composition.

In another embodiment, a polynucleotide attached to an electricalelement can be enzymatically ligated to a polynucleotide attached toanother element. Ligases are enzymes which repair damaged DNA. Anexample of a suitable ligase is T4 DNA ligase. In this embodiment, thepolynucleotides attached to each electrical element are double helixeswhich preferable have at least one cohesive, or sticky end, on the endof the duplex which is not attached to the electrical element. The term“cohesive end” refers to a single stranded polynucleotide which occursat the terminal end of a double helix. The cohesive end is typicallyfrom three to twenty, preferably three to eight, bases long and canhybridize to a complementary cohesive end. Once two complementarycohesive ends have hybridized a ligase can form covalent bonds betweenthe two duplexes.

The term “self-assembled polynucleotide” refers to either specifichybridization between polynucleotides attached to two differentelectrical elements or to hybridization of two cohesive ends followed byligation. A nanowire formed using a self-assembled polynucleotidetemplate is a self-assembled nanowire. Self-assembly of nanowires toform specific connection between electrical elements is expected tofacilitate the construction of nanometer-scale devices.

A redox monomer and a redox enzyme are added to the solution containingthe electrical elements having attached polynucleotide templates eithersimultaneously with the electrical elements or, preferably, after thepolynucleotides attached to the electrical elements have hybridized. Theredox monomers, for example, aniline monomers align along the hybridizedpolynucleotides to form a complex and are polymerized, therebyconnecting the electrical elements with a nanowire having a conductiveand/or optically active polymer complexed to a polynucleotide.

Another embodiment of the invention is a method of identifying a targetpolynucleotide by contacting the target polynucleotide with a probewhich includes a polynucleotide/conductive polymer complex that can bindto a target polynucleotide by hybridization. Hybridization of the probeto the target polynucleotide modifies at least one electromagneticproperty of the conductive polymer. Preferably, substituted orunsubstituted polyaniline is the conductive polymer. The probe can bindby hybridization to a target polynucleotide which is complementary, orsubstantially complementary, to the sequence, or a portion of thesequence, of the probe polynucleotide. The electromagnetic property ofthe conductive polymer which is modified is an optical and/or electricalproperty. The change in optical and/or electrical properties of theconductive polymer during or after hybridization with the target can beused in discriminating between perfectly complementary targets andtargets that have one or more mismatches. In another embodiment, theconductive polymer can be complexed to the target polynucleotide, aswell as the probe. In this embodiment, the conductive polymer isenzymatically polymerized on the target polynucleotic. The modifiedelectromagnetic property can be detected by a combination ofcharacterization methods that may include, but are not limited to,UV-visible absorption, circular dichroism and cyclic voltammetry. Thesecharacterization methods can be employed to estimate the extent ofhybridization. Discrimination between targets which are perfectlycomplementary to the probe and those which have one or more mismatchesmay also be discerned by monitoring the optical and/or electricalproperties during thermal melting of the hybridization complex of theprobe and the target. In addition, the polynucleotide/conductive polymercomplex of the probe may be may be attached to an electrical element.

A “polynucleotide” as used herein refers to single, double and triplestranded polynucleotides, as well as, quadruplexes. The polynucleotidein a polynucleotide/polyaniline complex can be a deoxyribonucleotides,ribonucleotides (hereinafter, “RNA”), modified polynucleotides, andpolynucleotide analogs such as peptide nucleic acid (hereinafter, “PNA”)and morpholino nucleic acids. In addition, a polynucleotide can becomposed of more than one polynucleotide molecule. For example, apolynucleotide duplex can be composed of two polynucleotides of the sametype (e.g., both ribonucleotides or both deoxyribonucleotides), or itcan be composed of a mixture of different types of polynucleotides(e.g., a combination of a ribonucleotide and a deoxyribonucleotide).

Complementary binding, or hybridization, is generally understood tooccur in an antiparallel manner, however, there are occasions in whichhybridization can occur in a parallel fashion, such as in a triplehelix, and this arrangement is also within the scope of the presentinvention. Hybridization is understood to essentially follow acomplementary pattern wherein a purine pairs with a pyrimidine viahydrogen bonds. More particularly, it is understood that whenhybridization occurs, complementary base-pairing of individual basepairs generally follows Chargaff's Rule wherein an adenine pairs with athymine (or uracil) and guanine pairs with cytosine. However,hybridization can occur between less than perfectly complementarysequences provided a stable binding complex is formed. The stability ofa binding complex is dependent on ionic strength, temperature and theconcentration of destabilizing agents such as urea and formamide in thehybridization medium, as well as, on factors such as the length of thepolynucleotide sequence, base composition, and percent mismatch betweenhybridizing sequences.

In addition, modified bases can account for unconventional base-pairing.A modified polynucleotide is understood to mean herein a DNA or RNApolynucleotide that contains chemically modified nucleotides. The term“polynucleotide analogue” is understood herein to denote non-nucleicacid molecules such as PNA (see Egholm, et al., J. Am. Chem. Soc.(1992), 114:1895, the teachings of which are incorporated herein byreference in their entirety) and morpholino antisense oligomers (seeSummerton and Weller, Antisense and Nucleic Acid Drug Dev. (1997),7:187, the teachings of which are incorporated herein by reference intheir entirety) that can engage in base-pairing interactions withconventional nucleic acids. These modified bases and polynucleotideanalogues are considered to be within the scope of the instantinvention. For example, polynucleotides containing deazaguaine anduracil bases can be used in place of guanine and thymine, respectively,to decrease the thermal stability of hybridized complex. Similarly,5-methylcytosine can be substituted for cytosine in hybrids if increasedthermal stability is desired. Modification to the sugar moiety can alsooccur and is embraced by the present invention. For example,modification to the ribose sugar moiety through the addition of2′-O-methyl groups which can be used to reduce the nucleasesusceptibility of RNA molecules. Modifications occurring with differentmoieties of the nucleic acid backbone are also within the scope of thisinvention. For example, the use of methyl phosphate or methylphosphonate linkages to remove negative charges from the phosphodiesterbackbone can be used.

Polynucleotides can bind to each other to form specific bindingcomplexes by complementary base-pairing interactions between thepolynucleotides. Possible base-pairing interactions useful in the methodinclude duplexes that have canonical Watson-Crick base-pairing (reviewedin Cantor and Schimmel, Biophysical Chemistry, Part I. The Conformationof Biological Macromolecules, Ch. 3 and 6, Freeman, San Francisco, 1980,the teachings of which are incorporated herein by reference in theirentirety) or noncanonical base-pairing schemes such as triple helixformation (Felsenfeld, Davies, and Rich, J. Am. Chem. Soc. (1957)79:2023; for review see Doronina and Behr, Chem. Soc. Rev. (1997), p.63-71, the teachings of which are incorporated herein by reference intheir entirety) and quadruplex formation (Sen and Gilbert, Nature (1990)344:410-414; Sen and Gilbert, Methods Enzymol. (1992) 211:191-9, theteachings of which are incorporated herein by reference in theirentirety). Methods for determining the thermal stability of a particularhybridization complex are well known in the literature (see Wetmur,Critical Reviews in Biochemistry and Molecular Biology, 26:227-259(1991); Quartin and Wetmur, Biochemistry, 28:1040-1047 (1989), theteachings of which are incorporated herein by reference in theirentirety).

The invention will now be further and more specifically described by thefollowing examples. All parts and percentages are by weight unlessotherwise specified.

EXAMPLES Example 1

A. Materials and Methods

Horseradish peroxidase (HRP) (enzyme classification number (EC)1.11.1.7), phosphate and Tris-HCl buffers were obtained from SigmaChemicals Company, St. Louis, Mo. Aniline, sulfonated polystyrene (SPS)and hydrogen peroxide (30%) were obtained from Aldrich Chemicals, Inc.,Milwaukee, Wis. All the chemicals were used as received.

B. Results and Discussion

The progress of a template-assisted polymerization reaction of anilinein the presence of the polyelectrolyte, sulfonated polystyrene (SPS) ina 1:1 ratio, was monitored by the change in visible absorbance. APerkin-Elmer Lambda-9® UV-Vis-near IR spectrophotometer was used for thespectral characterization of the polymer. FIG. 3 shows the visibleabsorption spectra of the sulfonated polystyrene/polyaniline (SPS/PA)complex prepared under various pH conditions of 4, 6, 8, and 10. Asshown in FIG. 3, SPS/PA, prepared at a pH of 4, exhibited a strongabsorbance maximum at approximately 780 mm. This was indicative of theemeraldine, or oxidized, electrically conducting form of polyaniline.Polymerization at higher pH resulted in an absorption maximum of about600 nm, indicating a more insulating form of polyaniline. In all cases,the polymer complex did not precipitate out of solution, indicating thatcomplexation of the polyaniline to the SPS had occurred.

Optimization of the molar ratio of monomer to polyelectrolyte template(repeat unit) was carried out. FIG. 4 shows a plot of absorption maximafor various SPS/aniline ratios. As shown, a ratio of 1:2, SPS/anilinewas the minimum ratio required to obtain the electrically conductingform of polyaniline, which had an absorption maximum at approximately780 nm at a pH in a range of between about 4 and about 5.

The reversible reduction/oxidation (redox) behavior of the SPS/PAcomplex was monitored by measuring visible absorption of the complexunder various pH conditions. In all cases the polymer complex wasprepared at pH 4.0 to obtain the electrically active form of thepolyaniline and then the pH of the solution was adjusted for theabsorption maxima measurements. As shown in FIG. 5A, the SPS/PA complexshifted in absorption maxima to shorter wavelengths as the pH of thesolution was increased. This was indicative of reduction of thepolyaniline backbone to a more insulating state. FIG. 5B shows thereverse behavior where the absorption maximum was found to shift back tolonger wavelengths with decreasing pH conditions. This was indicative ofoxidation of the polyaniline backbone back to a more electricallyconductive state. This reversible redox behavior was repeatable andconfirms that an electrically active form of polyaniline was present inthe final SPS/PA template complex. Molecular weight determination wascarried out by column chromatography using Protein PAK 300 SW®-WatersAssociation columns. Molecular weights of approximately 74,000 Daltonswere measured indicating polymerization of the aniline and complexationto the SPS template.

C. Thin Films by Layer-by-Layer Technique

Self-assembly of the SPS/PA complex onto glass slides was carried out bythe layer-by-layer electrostatic deposition technique (Ferreira, M., etal., Thin Solid Films (1995), 244:806 and Decher, G., et al., Thin SolidFilm, (1992), 210-211, the teachings of which are incorporated herein byreference in their entirety). A glass slide treated with alkali(Chemsolv® alkaline) was exposed to polycation and polyanion solutionsrepeatedly to transfer monolayers of these polyelectrolytes per everyexposure. 1 mg/ml solution of poly(diallyl dimethyl ammonium chloride)(PDAC) at pH 2.5 was used as the polycation while approximately 1 mg/mlsolution of SPS/PA at pH 2.5 was used as the polyanion. The glass slidewas exposed to each polyelectrolyte solution for 10 minutes and washedwith water at the same pH to remove the unbound polymer from thesurface. This process was repeated to obtain the desired number oflayers.

FIGS. 6 a and 6 b show the visible absorption spectra of a film of fiftybilayers wherein PDAC layers alternate with SPS/PA layers, under variouspH conditions. As shown in the figures, the multilayer film exhibitedsimilar redox behavior as was observed previously with the solutionabsorption spectra. This confirmed that facile electrostatic depositionwas feasible with the SPS/PA polymer complex and that the electricalactivity was maintained after deposition. In addition, multilayer andbulk films were prepared on indium tin oxide (ITO) slides and four-pointprobe conductivity measurements were taken. The results gavepolymer-complex conductivities in the range of 10³ to 10² S/cm.

Example 2

A. Materials and Methods

Horseradish peroxidase (HRP) (enzyme classification number (EC)1.11.1.7), phosphate and Tris-HCl buffers were obtained from SigmaChemicals Company, St. Louis, Mo. Phenol, sulfonated polystyrene (SPS)and hydrogen peroxide (30%) were obtained from Aldrich Chemicals, Inc.,Milwaukee, Wis. All the chemicals were used as received.

B. Results and Discussion

The progress of a template-assisted polymerization reaction of phenol inthe presence of the polyelectrolyte, sulfonated polystyrene (SPS) in a1:1 ratio, was monitored by the change in visible absorbance.Perkin-Elmer Lambda-9® UV-Vis-near IR spectrophotometer was used for thespectral characterization of the polymer. FIG. 7A shows the visibleabsorption of polyphenol without SPS, versus phenol monomer. As shown,there was a significant absorption maximum in the visible spectrum uponpolymerization, indicating formation of polyphenol. However, with timethe polymer began to precipitate out of solution. FIG. 7B shows thevisible absorption of polyphenol with SPS, versus phenol monomer. Asshown again, there was a significant absorption maximum of thepolymerized system in the visible spectrum. In this case, there was noobserved precipitation of the polymer complex out of solution.

Molecular weight determination was carried out by column chromatographyusing Protein PAk 300 SW® columns manufactured by Waters Association.Molecular weights as large as 136,000 Daltons were measured, indicatingpolymerization of the phenol and complexation to the SPS template.

Example 3

A. Preparation of DNA-Polyaniline Complex

Horseradish peroxidase (HRP, EC 1.11.1.7) type II, (150-200 units/mg)solid was purchased from Sigma Chemical Co. (St. Louis, Mo.). CalfThymus DNA was purchased from Worthington Biochemical Corporation(Freehold, N.J.). Aniline monomer (purity 99.5%) and hydrogen peroxide(30% by weight) were purchased from Aldrich Chemicals, Inc., Milwaukee,Wis., and were used as received. All other chemicals were of reagentgrade or better. All glassware and plasticware were sterilized byautoclaving for 30 minutes.

A stock solution of calf Thymus DNA (19.9 mg) was dissolved in 40 ml ofsterile, 10 mM sodium citrate buffer maintained at pH 4. The solutionwas stored in the refrigerator for 48 hours before reaction. Theconcentration of DNA was determined by the UV absorbance at 258 nm. Themolar extinction coefficient (ε) at 258 nm was taken as 6420 1 mol cm⁻¹,as reported by Sprecher, et al., Biopolymers (1979), 18:1009. Thereaction mixture had 10 ml of DNA stock solution, aniline in an amountequivalent to twice the molar concentration of DNA present in 10 ml andcatalytic amount of HRP (0.15 mg). The polymerization was carried out bythe dropwise addition of hydrogen peroxide (0.098 M), over a period of240 seconds. The total amount of hydrogen peroxide was limited to ⅕^(th)of the stoichiometric amount, calculated with respect to anilineconcentration. For synthesis in bulk, the polymerization was carried tocompletion and a stoichiometric amount of hydrogen peroxide was added.The DNA-polyaniline complex precipitates out from the mixture. Theprecipitate was washed several times using 1:1 mixture of acetone and pH4 water in order to remove residual aniline and low molecular weightpolyaniline. The gravimetric yield was 75%. Results of elementalanalysis of the DNA-polyaniline complex indicated C (46.8%), H (4.4%), P(5.45%). This indicated a ratio of 2.5:1 for DNA to aniline in thecomplex. The theoretically values calculated based on this ratio are C(43.2%), H (5.0%), N (13.1%), P (4.8%).

UV-Vis spectra and circular dichroism (CD) spectra were obtainedsimultaneously using Hewlett-Packard diode array detector photometer(type HP8452A) and Jasco CD spectrometer J-720, respectively. Theelemental analysis was performed by Schwarzkopf MicroanalyticalLaboratory, Woodside, N.Y.

B. Results and Discussion

At pH 4, the aniline molecules are protonated, and the electrostaticattraction between protonated aniline and the phosphate groups of theDNA helps in aligning the monomer on DNA (FIG. 8). The alignment of themonomer on the DNA promotes para-directed coupling of aniline moleculesduring polymerization (FIG. 2). The phosphate groups in the DNA matrixprovide a proton-rich environment that helps in accomplishingpolymerization of aniline at a significantly higher pH condition than ispossible in the absence of the DNA template. The polymerization iscatalyzed by HRP, and the polyaniline formed remains bound through ionicinteractions to the DNA.

C. Formation of Polyaniline on DNA (UV-Vis Spectra)

The UV-Vis spectra of DNA, DNA with aniline and HRP before and duringpolymerization are shown in FIG. 9. The addition of aniline and HRPincreased the absorption in the 200-280 nm range, while the absorptionin the visible region remained constant. UV-Vis spectra were recorded 5minutes after the addition of hydrogen peroxide and subsequently after20, 40, 60 and 80 minutes. The UV-Vis spectrum obtained after 5 minutesindicated absorption bands centered around 420 m polaron bands and 750nm bipolaron band. As time proceeded, the bipolaron band at 750 nmdiminished while the 420 nm and 310-320 nm bands increased in intensity.The 750 nm band have been attributed to presence of pernigraniline(quinoid form) of polyaniline. The penigraniline formed in the initialstages of the reaction was reduced to emeraldine salt by the addition ofaniline to growing polymer chain. This change was also accompanied by anincrease in absorbance in the region of 1000 nm. After 80 minutes, thesolution turned completely green, and the absorption spectra indicatedthe presence of polyaniline in the emeraldine salt form, which providedfurther evidence for the presence of polyaniline in the oxidized state.The DNA, thus provides the counter-ion and acts as a dopant for thepolyaniline.

D. Change in Cd Spectra During Polymerization

The CD spectra of Calf thymus DNA at pH 4, shown in FIG. 10, comparedwell with the already reported spectra, of DNA polymorph ‘B’. Thespectrum did not change with the addition of aniline and horseradishperoxidase. Very significant changes in the CD spectra were noticedafter 5 minutes, subsequent to the addition of hydrogen peroxide. The220 nm positive peak increased in intensity, while the 245 mm negativepeak reduced in intensity. The positive (Δε) shoulder at 270 nm changesto a new negative peak with fine structure. The positive peak at 275 nmreduced in intensity significantly. The CD spectra in the visible regionshowed the appearance of broad bands centered at 367 nm and 444 nm.

The CD spectra were measured until 80 minutes after the addition ofhydrogen peroxide. A comparison of the spectra of DNA-polyanilineobtained at 5 minutes and 80 minutes indicated very little changes inthe 200-320 nm region. It was concluded that changes in the secondarystructure of DNA occurred earlier than 5 minutes after the addition ofhydrogen peroxide. However, the positive, broad bands centered around367 nm and 444 nm increased in intensity steadily over time.

At pH 4, the polyaniline to remain charged and the phosphate groups inDNA provided the counterion for maintaining charge neutrality. Theshielding of phosphate groups by polyaniline induced a change in thesecondary structure of DNA leading to the formation of the over-woundpolymorph. On comparison with the earlier reports pertaining to changein secondary structure of Calf thymus DNA induced by the nature ofsolvent and concentration of salt (see Sprecher, et al., Biopolymers(1979), 18:1009; Bokma, et al., Biopolymers (1987), 26:893, theteachings of which are incorporated herein by reference in theirentirety), it was concluded that the formation of polyaniline caused achange similar to a ‘B’ to ‘C’ polymorphic transition. As a control, aDNA solution of same concentration was treated with 6 molar ammoniumfluoride. The shape of UV region of CD spectra of the DNA solutioncontaining 6 molar ammonium fluoride resembled that of DNA-polyaniline(FIG. 11). However, in the case of DNA-polyaniline, the concentration ofaniline used in the reaction was limited to a few millimoles. Yet thechanges in the CD spectrum were significant. This confirmed theformation of a polyelectrolyte complex of DNA-polyaniline.

The visible region of the CD spectrum provided interesting informationon the secondary structure of the polyaniline. The increase of the 367nm and 444 nm CD bands until 80 minutes indicated the development ofchirality in the polyaniline concomitant with the increase of molecularweight. Chirality/optically activity has been observed in chemically(Majidi, M. R., et al., Polymer (1995), 36:3597, the teachings of whichare incorporated herein by reference in their entirety) andelectrochemically (Majidi, M. R., et al., Polymer (1994), 35:3113, theteachings of which are incorporated herein by reference in theirentirety) synthesized complex and colloids (Barisci, J. N., et al.,Synth. Met. (1997), 84:181, the teachings of which are incorporatedherein by reference in their entirety) of polyaniline and (IR)-(−)10-Camphorsulfonic acid. The observed macroasymmetry of the polyanilinesalts formed in the presence of (+) or (−)-camphorsulfonic acid has beenrationalized in terms of the polyaniline chain adopting a preferredone-sense helical screw maintained by the dopant anions viaelectrostatic and H-bonding. It is therefore probable that theelectrostatic interactions between the DNA double helix and polyaniline,induced a macroasymmetry in the polyaniline.

The enzyme catalyzed synthesis described here, can be extended to thepolymerization of functional monomers (substituted phenols/anilines)with interesting optical and electrical properties. This method can alsobe extended to other ionic biological polyelectrolytes such as collagen.Chiral organization of polyaniline around DNA may enhancement in theelectrical conductivity of polyaniline. In addition, the chirality andelectrical properties of polyaniline combined with the selectivity ofDNA may be useful in the design of highly specific biosensors.

Example 4

A. Changes in Cd Spectra During Oxidation or Reduction of Polyaniline

The secondary structure of DNA was readily controlled by the changingthe extent of oxidation of polyaniline. The pH of the DNA-polyanilinesolution was changed from 4-10 by adding 1 M NaOH and the CD spectra wasobtained (FIG. 12A). It was evident that the CD spectra of DNA changedrapidly, and at pH 6, the DNA reverted back to its loosely wound state(‘B’ form). The neutralization of polyaniline minimized theelectrostatic interaction between the DNA and polyaniline resulting inthe uncoiling of DNA, back to its native state.

Evidence that the observed conformational changes were due to reductionof the polyaniline was obtained from the UV-Vis spectra (FIG. 13A). Adecrease and subsequent disappearance of the polaron bands at 404 and755 nm as the pH of the solution increased was observed. Simultaneously,the exciton transition of the quinoid rings at 564 nm and the ππ*transition of the benzenoid rings at 320 nm emerged. The solution wentthrough a series of color changes, from green to blue to purpleindicating the transition of the polyaniline to the emeraldine baseform. Two isobestic points at 354 nm and 458 nm were observed. Thechanges observed in the UV-Vis and the CD spectra under increasinglybasic conditions were consistent with partial unwinding of the DNAduplex as consequence of the reduction of polyaniline.

When DNA-polyaniline was reoxidized using HCl, it was observed that theCD spectrum approaches the original CD spectra of oxidizedDNA-polyaniline at pH 4 (FIG. 12B). The evidence for reoxidation ofpolyaniline was observed in the UV-Vis spectra (FIG. 13B) as indicatedby the recovery of polaron bands and the decrease of the excitontransition band. The average recovery of the CD bands at 290 nm, 285 nm,275 nm and 245 nm was greater than 50%. The same solution was reducedand reoxidized (taken to pH 10 and back to pH 4). CD spectra obtainedduring this process indicated a significantly better recovery (75%) inthe DNA region. Therefore, it was possible to reversibly change theconformation of the DNA (over-wind and unwind) by controlling the degreeof oxidation of polyaniline.

B. Control Experiments

Control experiments were performed by mixing a molecular complex ofpolystyrene sulfonic acid and polyaniline, with Calf thymus DNA. Therewas no observable change in the conformation of DNA. This experimentprovides unambiguous evidence for existence of polyaniline, closelybound to the DNA, only if the synthesis of polyaniline is performed inthe presence of DNA.

The present study has demonstrated the use of DNA as a substrate for thesynthesis of polymers with unique electrical and optical properties. Theconducting polymer (polyaniline) bound to the DNA can be used as a“tool” to manipulate the conformation of the DNA. In principle, thedoping, dedoping and redoping process and the conformational switchingcan also be accomplished electrochemically. This can enhance the speedand ease of doping/dedoping process. The remarkable specificity in therecognition capabilities of DNA can be combined with the dopingdependent electrical properties of polyaniline to develop methods forhighly selective DNA detection and biosensing.

Equivalents

While this invention has been particularly shown and described withreferences to preferred embodiments thereof, it will be understood bythose skilled in the art that various changes in form and details may bemade therein without departing from the scope of the inventionencompassed by the appended claims.

1. A composition of matter, comprising a polynucleotide template and asubstituted or unsubstituted polyaniline bound together as a complex,wherein the polyaniline has a chiral formation.
 2. The composition ofclaim 1 wherein the polynucleotide is a single strand.
 3. Thecomposition of claim 1, wherein the polynucleotide is a double helix. 4.The composition of claim 1, wherein the polynucleotide template is adeoxyribonucleotide.
 5. The composition of claim 1, wherein thepolynucleotide is a ribonucleotide.
 6. A method of preparing apolynucleotide/polyaniline complex, comprising combining a substitutedor unsubstituted aniline monomer, a polynucleotide template and a redoxenzyme, whereby the monomer aligns along the template to form a complexand polymerizes to form a polyaniline, thereby forming thepolynucleotide/polyaniline complex.
 7. The method of claim 6, whereinthe polynucleotide is a deoxyribonucleotide or a ribonucleotide.
 8. Themethod of claim 6, wherein the enzyme is a peroxidase.
 9. The method ofclaim 8, wherein the peroxidase is horseradish peroxidase.
 10. Themethod of claim 8, wherein hydrogen peroxide is combined with theaniline monomer, polynucleotide template and a redox enzyme.
 11. Themethod of claim 8, wherein the polynucleotide template and redox enzymeare combined in a solution having a pH of about 4 to about
 5. 12. Themethod of claim 6, wherein the polynucleotide is a single strand. 13.The method of claim 6, wherein the polynucleotide is a double helix. 14.The method of claim 13, wherein the polyaniline formed has a chiralconformation.
 15. The method of claim 13, wherein the polyaniline formedhas an achiral conformation.
 16. A method of modulating the conformationof a polynucleotide which is bound to a conductive polymer in a complex,comprising changing the oxidation state of the conductive polymer. 17.The method of claim 16, wherein the conductive polymer is selected fromthe group consisting of: a substituted or unsubstituted polyaniline or asubstituted or unsubstituted polyphenol.
 18. The method of claim 17,wherein the conductive polymer is polyaniline.
 19. The method of claim18, wherein the polynucleotide is a single strand.
 20. The method ofclaim 18, wherein the polynucleotide is a double helix.
 21. The methodof claim 20, wherein the oxidation state of the polyaniline is changedby oxidizing said polyaniline, thereby causing the double helix to havemore base pairs per helical repeat after the polyaniline is oxidized.22. The method of claim 21, further comprising the step of reducing thepolyaniline, thereby causing the double helix to have less base pairsper helical repeat after the polyaniline is reduced.
 23. The method ofclaim 22, wherein the oxidation state of polyaniline is changedelectrochemically.
 24. The method of claim 20, wherein the oxidationstate of the polyaniline is changed by reducing said polyaniline,thereby causing the double helix to have fewer base pairs per helicalrepeat after the polyaniline is reduced.
 25. The method of claim 24,further comprising the step of oxidizing the polyaniline, therebycausing the double helix to have more base pairs per helical repeatafter the polyaniline is oxidized.
 26. The method of claim 22 or 25,wherein the polyaniline is cyclically oxidized and reduced.
 27. Themethod of claim 25, wherein the oxidation state of polyaniline ischanged electrochemically.
 28. An electrical component, comprising: a)an electrical element; and b) a nanowire attached to the electricalelement, wherein said nanowire includes a polynucleotide template and aconductive polymer bound together as a complex.
 29. The electricalcomponent of claim 28, wherein the conductive polymer is selected fromthe group consisting of: a substituted or unsubstituted polyaniline or asubstituted or unsubstituted polyphenol.
 30. The electrical component ofclaim 29, wherein the conductive polymer is polyaniline.
 31. Theelectrical component of claim 30, wherein the polynucleotide in thepolynucleotide/polyaniline complex is a single strand.
 32. Theelectrical component of claim 30, wherein the polynucleotide in thepolynucleotide/polyaniline complex is a double helix.
 33. The electricalcomponent of claim 30, wherein a portion of the polynucleotide in thepolynucleotide/polyaniline complex is single stranded and a portion is adouble helix.
 34. The electrical component of claim 28, furtherincluding at least one other electrical element, and wherein theelectrical elements are connected by said nanowire.
 35. The electricalcomponent of claim 34, wherein the polynucleotide/polyaniline complexincludes two or more polynucleotides that are hybridized.
 36. Theelectrical component of claim 35, wherein the polynucleotides in thepolynucleotide/polyaniline complex are deoxyribonucleotides.
 37. Theelectrical component of claim 35, wherein the polynucleotides in thepolynucleotide/polyaniline complex are ribonucleotides.
 38. Theelectrical component of claim 35, wherein the polynucleotides in thepolynucleotide/polyaniline complex are a combination ofdeoxyribonucleotides and ribonucleotides.
 39. The electrical componentof claim 34, wherein the polynucleotide/polyaniline complex includes twoor more polynucleotides that have been assembled by enzymatic ligation.40. A method of forming an electrically conductive connection betweenelectrical elements, comprising the steps of: a) connecting at least twoelectrical elements with a polynucleotide; and b) contacting thepolynucleotide with a redox monomer and a redox enzyme, whereby themonomer aligns along the template to form a complex and polymerizes toform a conductive polymer, thereby forming a polynucleotide/conductivepolymer complex that electrically connects the electrical elements, saidpolynucleotide/conductive polymer complex being electrically conductive.41. The method of claim 40, wherein the conductive polymer is selectedfrom the group consisting of: a substituted or unsubstituted polyanilineor a substituted or unsubstituted polyphenol.
 42. The method of claim41, wherein the conductive polymer is polyaniline.
 43. The method ofclaim 40, wherein the electrical elements are connected by hybridizationof a first polynucleotide, connected to a first electrical element, witha second polynucleotide, connected to a second electrical element. 44.The method of claim 40, wherein the electrical elements are connected byligation of a first polynucleotide, connected to a first electricalelement, to a second polynucleotide, connected to a second electricalelement.
 45. The method of claim 40, wherein the redox enzyme is aperoxidase.
 46. The method of claim 45, wherein the peroxidase ishorseradish peroxidase.
 47. The method of claim 45, wherein hydrogenperoxide is combined with the polynucleotide, redox monomer and redoxenzyme.
 48. The method of claim 40, wherein the polymerization of theaniline monomer is conducted in a solution having a pH of about 4 toabout
 5. 49. The method of claim 43, wherein the electrical elements areconnected by hybridization of the first and second polynucleotidesbefore contacting the hybridized polynucleotides with the redox monomerand the redox enzyme.
 50. The method of claim 43, wherein the electricalelements are connected by hybridization of the first and secondpolynucleotides simultaneously with contacting the polynucleotides withthe redox monomer and the redox enzyme.
 51. A method for identifying atarget polynucleotide, comprising the steps of: a) combining said targetpolynucleotide with a probe that includes a polynucleotide templatecomplexed with a conductive polymer, whereby said probe hybridizes withthe target polynucleotide, said hybridization modifying at least oneelectromagnetic property of the conductive polymer; and b) detectingsaid modified electromagnetic property, thereby identifying the targetpolynucleotide.
 52. The method of claim 51, wherein the conductivepolymer is a substituted or unsubstituted polyaniline.
 53. The method ofclaim 51, wherein the electromagnetic property is an electrical oroptical property.
 54. The method of claim 53, wherein the modifiedelectromagnetic property is detected using UV-Visible absorption,circular dichroism or cyclic voltammetry.
 55. The method of claim 53,wherein the probe is attached to an electrical element.